From 5cd07393baa1d223d1019dc19d4539ce16f14865 Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 12:00:25 +0200
Subject: [PATCH 01/15] printing requested gene list

---
 bin/DESeq2.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index e15688fb..da993709 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -413,6 +413,8 @@ if (!is.null(opt$genelist)){
   requested_genes_plot <- subset(gene_names, gene_name %in% gene_ids$requested_gene_name)
 
   # Check that genes are in the cds table
+  print("Requested_genes_plot")
+  print(requested_genes_plot)
   requested_genes_plot <- requested_genes_plot[which(requested_genes_plot$Ensemble_ID %in% row.names(cds)),]
   requested_genes_plot_Ensembl <- requested_genes_plot$Ensembl_ID
   requested_genes_plot_gene_name <- requested_genes_plot$gene_name

From ea617e04a75eb4822e7dbe298d4dcbea56514d5e Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 12:16:41 +0200
Subject: [PATCH 02/15] bump versions 1.3.1

---
 .github/workflows/ci.yml |  8 ++++----
 CHANGELOG.md             | 12 +++++++++++-
 environment.yml          |  2 +-
 3 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 96e32615..31ed3ead 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -31,13 +31,13 @@ jobs:
 
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t qbicpipelines/rnadeseq:1.2.0
+        run: docker build --no-cache . -t qbicpipelines/rnadeseq:dev
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull qbicpipelines/rnadeseq:dev
-          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:1.2.0
+          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:dev
 
       - name: Install Nextflow
         run: |
@@ -69,13 +69,13 @@ jobs:
       
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t qbicpipelines/rnadeseq:1.2.0
+        run: docker build --no-cache . -t qbicpipelines/rnadeseq:dev
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull qbicpipelines/rnadeseq:dev
-          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:1.2.0
+          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:dev
 
       - name: Install Nextflow
         run: |
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5e1595bd..447b4784 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,16 @@
 # qbic-pipelines/rnadeseq: Changelog
 
-## 1.3.0 - dev
+## 1.3.1 - dev
+
+### Added
+
+- Bump versions to 1.3.1dev
+
+### Fixed
+
+### Changed
+
+## 1.3.0 - Almond Blossoms
 
 ### Added
 
diff --git a/environment.yml b/environment.yml
index cf6a1617..feaee925 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,7 +1,7 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
 # use this to find packages: https://anaconda.org/
-name: qbic-pipelines-rnadeseq-1.3.0dev
+name: qbic-pipelines-rnadeseq-1.3.1dev
 channels:
   - conda-forge
   - bioconda

From 9c911b37cabf6ef32e398f11d5566961cb158101 Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 14:53:37 +0200
Subject: [PATCH 03/15] bump versions

---
 Dockerfile      | 4 ++--
 nextflow.config | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 37be02c5..87aa07e8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -9,10 +9,10 @@ RUN apt-get update -qq && \
     apt-get install -y zip procps ghostscript
 
 # Add conda installation dir to PATH
-ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-1.3.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-1.3.1dev/bin:$PATH
 
 # Dump the details of the installed packates to a file for posterity
-RUN conda env export --name qbic-pipelines-rnadeseq-1.3.0dev > qbic-pipelines-rnadeseq-1.3.0dev.yml
+RUN conda env export --name qbic-pipelines-rnadeseq-1.3.1dev > qbic-pipelines-rnadeseq-1.3.1dev.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local config
 RUN touch .Rprofile
diff --git a/nextflow.config b/nextflow.config
index dd61de67..c1296e77 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -102,7 +102,7 @@ manifest {
   description = 'Downstream differential gene expression analysis with DESeq2'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.04'
-  version = '1.3.0dev'
+  version = '1.3.1dev'
 }
 
 // Function to ensure that resource requirements don't go beyond

From 0522c7451e673abfbe8b38307c3c89d7e32ff437 Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 15:38:29 +0200
Subject: [PATCH 04/15] debug boxplots

---
 bin/DESeq2.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index da993709..7a73577b 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -413,13 +413,15 @@ if (!is.null(opt$genelist)){
   requested_genes_plot <- subset(gene_names, gene_name %in% gene_ids$requested_gene_name)
 
   # Check that genes are in the cds table
+
+  requested_genes_plot <- requested_genes_plot[which(requested_genes_plot$Ensemble_ID %in% row.names(cds)),]
   print("Requested_genes_plot")
   print(requested_genes_plot)
-  requested_genes_plot <- requested_genes_plot[which(requested_genes_plot$Ensemble_ID %in% row.names(cds)),]
   requested_genes_plot_Ensembl <- requested_genes_plot$Ensembl_ID
   requested_genes_plot_gene_name <- requested_genes_plot$gene_name
 
   for (i in requested_genes_plot_Ensembl){
+    print(i)
     boxplot_counts <- plotCounts(cds, gene=i, intgroup=c("combfactor"), returnData=TRUE, normalized = T)
     boxplot_counts$variable = row.names(boxplot_counts)
     plot <- ggplot(data=boxplot_counts, aes(x=combfactor, y=count, fill=combfactor)) +

From 0e21c4f572588a8a95c0344b78d75d9cae475fe3 Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 15:39:50 +0200
Subject: [PATCH 05/15] debug boxplots

---
 bin/DESeq2.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index 7a73577b..f42b5bf2 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -417,6 +417,8 @@ if (!is.null(opt$genelist)){
   requested_genes_plot <- requested_genes_plot[which(requested_genes_plot$Ensemble_ID %in% row.names(cds)),]
   print("Requested_genes_plot")
   print(requested_genes_plot)
+  print("row_names")
+  print(row.names(cds))
   requested_genes_plot_Ensembl <- requested_genes_plot$Ensembl_ID
   requested_genes_plot_gene_name <- requested_genes_plot$gene_name
 

From 17fdf563d5ab13d6414b6c8b3e2e89558a4b9cc3 Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 15:47:08 +0200
Subject: [PATCH 06/15] debug boxplots

---
 bin/DESeq2.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index f42b5bf2..2944af73 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -413,10 +413,10 @@ if (!is.null(opt$genelist)){
   requested_genes_plot <- subset(gene_names, gene_name %in% gene_ids$requested_gene_name)
 
   # Check that genes are in the cds table
-
-  requested_genes_plot <- requested_genes_plot[which(requested_genes_plot$Ensemble_ID %in% row.names(cds)),]
   print("Requested_genes_plot")
   print(requested_genes_plot)
+  requested_genes_plot <- requested_genes_plot[which(requested_genes_plot$Ensemble_ID %in% row.names(cds)),]
+
   print("row_names")
   print(row.names(cds))
   requested_genes_plot_Ensembl <- requested_genes_plot$Ensembl_ID

From e28bbe9186d5215197f5a2bacfcfd09e01720bbe Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 15:55:44 +0200
Subject: [PATCH 07/15] fix boxplot

---
 bin/DESeq2.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index 2944af73..35515a3b 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -415,7 +415,7 @@ if (!is.null(opt$genelist)){
   # Check that genes are in the cds table
   print("Requested_genes_plot")
   print(requested_genes_plot)
-  requested_genes_plot <- requested_genes_plot[which(requested_genes_plot$Ensemble_ID %in% row.names(cds)),]
+  requested_genes_plot <- subset(requested_genes_plot, Ensemble_ID %in% row.names(cds))
 
   print("row_names")
   print(row.names(cds))

From 4cf7420ce26eaa878bec2f965e0c4e17dbc5d8ca Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 15:58:12 +0200
Subject: [PATCH 08/15] fix boxplot

---
 bin/DESeq2.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index 35515a3b..e623c01e 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -415,7 +415,7 @@ if (!is.null(opt$genelist)){
   # Check that genes are in the cds table
   print("Requested_genes_plot")
   print(requested_genes_plot)
-  requested_genes_plot <- subset(requested_genes_plot, Ensemble_ID %in% row.names(cds))
+  requested_genes_plot <- subset(requested_genes_plot, requested_genes_plot$Ensemble_ID %in% row.names(cds))
 
   print("row_names")
   print(row.names(cds))

From f44a8c09720ff052dc586d278375613736d7f467 Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 16:26:42 +0200
Subject: [PATCH 09/15] fix boxplot

---
 bin/DESeq2.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index e623c01e..dd4cce8c 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -415,7 +415,10 @@ if (!is.null(opt$genelist)){
   # Check that genes are in the cds table
   print("Requested_genes_plot")
   print(requested_genes_plot)
-  requested_genes_plot <- subset(requested_genes_plot, requested_genes_plot$Ensemble_ID %in% row.names(cds))
+  requested_genes_plot <- subset(requested_genes_plot, requested_genes_plot$Ensembl_ID %in% row.names(cds))
+
+  print("Subset requested genes plot")
+  print(requested_genes_plot)
 
   print("row_names")
   print(row.names(cds))

From c4af300dbc5724104c4467935ded113601d1e618 Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 16:42:09 +0200
Subject: [PATCH 10/15] fix boxplot requested

---
 bin/DESeq2.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index dd4cce8c..ab5f8967 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -420,14 +420,14 @@ if (!is.null(opt$genelist)){
   print("Subset requested genes plot")
   print(requested_genes_plot)
 
-  print("row_names")
+  print("row_names")gg
   print(row.names(cds))
   requested_genes_plot_Ensembl <- requested_genes_plot$Ensembl_ID
   requested_genes_plot_gene_name <- requested_genes_plot$gene_name
 
-  for (i in requested_genes_plot_Ensembl){
-    print(i)
-    boxplot_counts <- plotCounts(cds, gene=i, intgroup=c("combfactor"), returnData=TRUE, normalized = T)
+  for (i in c(1,length(requested_genes_plot_Ensembl)){
+    print(requested_genes_plot_Ensembl[i])
+    boxplot_counts <- plotCounts(cds, gene=requested_genes_plot_Ensembl[i], intgroup=c("combfactor"), returnData=TRUE, normalized = T)
     boxplot_counts$variable = row.names(boxplot_counts)
     plot <- ggplot(data=boxplot_counts, aes(x=combfactor, y=count, fill=combfactor)) +
       geom_boxplot(position=position_dodge()) +

From 3f48626dc77a5496ffdb84190aed757dba8c8aec Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 16:44:31 +0200
Subject: [PATCH 11/15] fix boxplots for real

---
 bin/DESeq2.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index ab5f8967..a9c41475 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -420,7 +420,7 @@ if (!is.null(opt$genelist)){
   print("Subset requested genes plot")
   print(requested_genes_plot)
 
-  print("row_names")gg
+  print("row_names")
   print(row.names(cds))
   requested_genes_plot_Ensembl <- requested_genes_plot$Ensembl_ID
   requested_genes_plot_gene_name <- requested_genes_plot$gene_name

From 55660f4c9a08ce253c11393c21fccb60ace84bef Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 16:56:24 +0200
Subject: [PATCH 12/15] fix boxplots now really

---
 bin/DESeq2.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index a9c41475..7965b44a 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -425,7 +425,7 @@ if (!is.null(opt$genelist)){
   requested_genes_plot_Ensembl <- requested_genes_plot$Ensembl_ID
   requested_genes_plot_gene_name <- requested_genes_plot$gene_name
 
-  for (i in c(1,length(requested_genes_plot_Ensembl)){
+  for (i in c(1,length(requested_genes_plot_Ensembl))){
     print(requested_genes_plot_Ensembl[i])
     boxplot_counts <- plotCounts(cds, gene=requested_genes_plot_Ensembl[i], intgroup=c("combfactor"), returnData=TRUE, normalized = T)
     boxplot_counts$variable = row.names(boxplot_counts)

From 24bf90eecd5dba66f3aed3f46a6851428eff7275 Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 17:03:10 +0200
Subject: [PATCH 13/15] really really fix boxlplots

---
 bin/DESeq2.R | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index 7965b44a..d02f6857 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -420,12 +420,10 @@ if (!is.null(opt$genelist)){
   print("Subset requested genes plot")
   print(requested_genes_plot)
 
-  print("row_names")
-  print(row.names(cds))
   requested_genes_plot_Ensembl <- requested_genes_plot$Ensembl_ID
   requested_genes_plot_gene_name <- requested_genes_plot$gene_name
 
-  for (i in c(1,length(requested_genes_plot_Ensembl))){
+  for (i in c(1:length(requested_genes_plot_Ensembl))){
     print(requested_genes_plot_Ensembl[i])
     boxplot_counts <- plotCounts(cds, gene=requested_genes_plot_Ensembl[i], intgroup=c("combfactor"), returnData=TRUE, normalized = T)
     boxplot_counts$variable = row.names(boxplot_counts)

From d9be7b2f7e5bd9a8dc6fa358b150de0ddcc1fd26 Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 17:14:01 +0200
Subject: [PATCH 14/15] finally fix bug boxplots

---
 CHANGELOG.md | 2 ++
 bin/DESeq2.R | 9 +++------
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 447b4784..eb20cf34 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,8 @@
 
 ### Fixed
 
+- Fix bug plots requested boxplots
+
 ### Changed
 
 ## 1.3.0 - Almond Blossoms
diff --git a/bin/DESeq2.R b/bin/DESeq2.R
index d02f6857..69d00fed 100755
--- a/bin/DESeq2.R
+++ b/bin/DESeq2.R
@@ -205,6 +205,7 @@ if (!is.null(opt$contrasts_matrix)){
 
     contname <- names(contrasts[i])
     results_DEseq_contrast <- as.data.frame(results_DEseq_contrast)
+    print("Analyzing contrast:")
     print(contname)
     # Add gene name in table
     DE_genes_contrast_genename <- results_DEseq_contrast
@@ -268,6 +269,7 @@ if (!is.null(opt$contrasts_pairs)) {
       } 
       results_DEseq_contrast <- results(cds, contrast=list(cont[1],cont[2]))
       results_DEseq_contrast <- as.data.frame(results_DEseq_contrast)
+      print("Analyzing contrast:")
       print(contname)
       # Add gene name in table
       DE_genes_contrast_genename <- results_DEseq_contrast
@@ -294,6 +296,7 @@ if (is.null(opt$contrasts_matrix) & is.null(opt$contrasts_list) & is.null(opt$co
   for (contname in contrast_names) {
     results_DEseq_contrast <- results(cds, name=contname)
     results_DEseq_contrast <- as.data.frame(results_DEseq_contrast)
+    print("Analyzing contrast:")
     print(contname)
 
     # Adding gene name to table
@@ -413,18 +416,12 @@ if (!is.null(opt$genelist)){
   requested_genes_plot <- subset(gene_names, gene_name %in% gene_ids$requested_gene_name)
 
   # Check that genes are in the cds table
-  print("Requested_genes_plot")
-  print(requested_genes_plot)
   requested_genes_plot <- subset(requested_genes_plot, requested_genes_plot$Ensembl_ID %in% row.names(cds))
 
-  print("Subset requested genes plot")
-  print(requested_genes_plot)
-
   requested_genes_plot_Ensembl <- requested_genes_plot$Ensembl_ID
   requested_genes_plot_gene_name <- requested_genes_plot$gene_name
 
   for (i in c(1:length(requested_genes_plot_Ensembl))){
-    print(requested_genes_plot_Ensembl[i])
     boxplot_counts <- plotCounts(cds, gene=requested_genes_plot_Ensembl[i], intgroup=c("combfactor"), returnData=TRUE, normalized = T)
     boxplot_counts$variable = row.names(boxplot_counts)
     plot <- ggplot(data=boxplot_counts, aes(x=combfactor, y=count, fill=combfactor)) +

From c7854729793c3de0b9552a3dea7d046270d4c2cc Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Wed, 30 Sep 2020 17:18:30 +0200
Subject: [PATCH 15/15] bump versions 1.3.1

---
 .github/workflows/ci.yml | 8 ++++----
 CHANGELOG.md             | 4 ++--
 Dockerfile               | 4 ++--
 environment.yml          | 2 +-
 nextflow.config          | 4 ++--
 5 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 31ed3ead..d6b0e477 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -31,13 +31,13 @@ jobs:
 
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t qbicpipelines/rnadeseq:dev
+        run: docker build --no-cache . -t qbicpipelines/rnadeseq:1.3.1
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull qbicpipelines/rnadeseq:dev
-          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:dev
+          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:1.3.1
 
       - name: Install Nextflow
         run: |
@@ -69,13 +69,13 @@ jobs:
       
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t qbicpipelines/rnadeseq:dev
+        run: docker build --no-cache . -t qbicpipelines/rnadeseq:1.3.1
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull qbicpipelines/rnadeseq:dev
-          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:dev
+          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:1.3.1
 
       - name: Install Nextflow
         run: |
diff --git a/CHANGELOG.md b/CHANGELOG.md
index eb20cf34..2db2bdf1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,10 +1,10 @@
 # qbic-pipelines/rnadeseq: Changelog
 
-## 1.3.1 - dev
+## 1.3.1 - Almond Blossoms hotfix
 
 ### Added
 
-- Bump versions to 1.3.1dev
+- Bump versions to 1.3.1
 
 ### Fixed
 
diff --git a/Dockerfile b/Dockerfile
index 87aa07e8..90c41f46 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -9,10 +9,10 @@ RUN apt-get update -qq && \
     apt-get install -y zip procps ghostscript
 
 # Add conda installation dir to PATH
-ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-1.3.1dev/bin:$PATH
+ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-1.3.1/bin:$PATH
 
 # Dump the details of the installed packates to a file for posterity
-RUN conda env export --name qbic-pipelines-rnadeseq-1.3.1dev > qbic-pipelines-rnadeseq-1.3.1dev.yml
+RUN conda env export --name qbic-pipelines-rnadeseq-1.3.1 > qbic-pipelines-rnadeseq-1.3.1.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local config
 RUN touch .Rprofile
diff --git a/environment.yml b/environment.yml
index feaee925..545bd9cd 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,7 +1,7 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
 # use this to find packages: https://anaconda.org/
-name: qbic-pipelines-rnadeseq-1.3.1dev
+name: qbic-pipelines-rnadeseq-1.3.1
 channels:
   - conda-forge
   - bioconda
diff --git a/nextflow.config b/nextflow.config
index c1296e77..b11ac92a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -46,7 +46,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'qbicpipelines/rnadeseq:dev'
+process.container = 'qbicpipelines/rnadeseq:1.3.1'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -102,7 +102,7 @@ manifest {
   description = 'Downstream differential gene expression analysis with DESeq2'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.04'
-  version = '1.3.1dev'
+  version = '1.3.1'
 }
 
 // Function to ensure that resource requirements don't go beyond